The livestock exporter, Wellard, says it was confident the welfare of thousands of sheep would be guaranteed when they were sent to Pakistan.

Wellard's Karachi importer has confirmed more than half of the 21,000 Australian sheep sent to Pakistan earlier this month have been slaughtered by authorities in an inhumane manner.

The importer, PK Meat and Food Company, bought the sheep after authorities in Bahrain rejected the shipment on the grounds they were infected.

Wellard's Steven Meerwald says his company has been sending sheep safely to its commercial partner in Karachi for more than a decade, and the mass slaughter was the result of unprecedented government intervention.

"This is akin to having a cruise ship hijacked," he said.

"You lose absolute control because the pirates are in charge and this has been the case."

A Pakistani court will resume today to decide the fate of the remaining sheep after the cull was suspended earlier this week.

The Federal Opposition is urging the Agriculture Minister to consider travelling to Pakistan to deal directly with the reports of animal cruelty.

The Coalition's agriculture spokesman John Cobb says while it is difficult to assess the allegations without having full knowledge of the facts, he says it is important the Government takes a lead role in dealing with the concerns.

"This does sound like one of those special cases where it requires personal contact from a Minister of the Crown to find out what's going on and hopefully have it dealt with," he said.